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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.7.dev0

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        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2018-10-23, 19:39 based on data in: /share/lasallelab/Annie/Ashwood_humanMacrophages/fastqc_pretrim


        General Statistics

        Showing 423/423 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        101119LPS_S137_L001_R1_001
        30.4%
        34%
        1.6
        101119LPS_S160_L006_R1_001
        28.6%
        35%
        2.2
        101119LPS_S160_L007_R1_001
        28.6%
        35%
        2.2
        101119LTA_S25_L006_R1_001
        26.5%
        36%
        2.0
        101119LTA_S25_L007_R1_001
        26.6%
        36%
        2.0
        101119LTA_S2_L001_R1_001
        29.0%
        35%
        1.5
        101119NT_S136_L001_R1_001
        40.6%
        38%
        1.2
        101119NT_S159_L006_R1_001
        43.1%
        39%
        1.9
        101119NT_S159_L007_R1_001
        43.0%
        39%
        1.9
        101123LPS_S26_L006_R1_001
        33.7%
        34%
        1.8
        101123LPS_S26_L007_R1_001
        33.8%
        34%
        1.8
        101123LPS_S3_L001_R1_001
        32.8%
        33%
        1.2
        101123LTA_S117_L006_R1_001
        34.6%
        35%
        2.0
        101123LTA_S117_L007_R1_001
        34.5%
        34%
        2.0
        101123LTA_S94_L001_R1_001
        34.6%
        33%
        1.3
        101123NT_S1_L001_R1_001
        40.2%
        36%
        1.3
        101123NT_S24_L006_R1_001
        43.9%
        38%
        2.0
        101123NT_S24_L007_R1_001
        43.8%
        38%
        2.0
        101132LPS_S122_L006_R1_001
        46.0%
        36%
        2.1
        101132LPS_S122_L007_R1_001
        46.2%
        36%
        2.1
        101132LPS_S99_L001_R1_001
        44.5%
        35%
        1.5
        101132LTA_S114_L006_R1_001
        24.6%
        35%
        1.3
        101132LTA_S114_L007_R1_001
        24.9%
        35%
        1.3
        101132LTA_S91_L001_R1_001
        44.6%
        34%
        3.9
        101132NT_S73_L001_R1_001
        37.0%
        36%
        1.2
        101132NT_S96_L006_R1_001
        38.3%
        37%
        1.8
        101132NT_S96_L007_R1_001
        38.4%
        37%
        1.7
        101134LPS_S127_L001_R1_001
        32.1%
        32%
        1.6
        101134LPS_S150_L006_R1_001
        29.1%
        33%
        2.1
        101134LPS_S150_L007_R1_001
        29.2%
        33%
        2.1
        101134LTA_S118_L001_R1_001
        29.7%
        33%
        1.1
        101134LTA_S141_L006_R1_001
        27.4%
        34%
        1.6
        101134LTA_S141_L007_R1_001
        27.4%
        34%
        1.6
        101134NT_S101_L001_R1_001
        35.3%
        36%
        1.3
        101134NT_S124_L006_R1_001
        36.0%
        37%
        1.8
        101134NT_S124_L007_R1_001
        36.1%
        37%
        1.8
        101138LPS_S112_L006_R1_001
        22.6%
        35%
        1.6
        101138LPS_S112_L007_R1_001
        22.7%
        35%
        1.6
        101138LPS_S89_L001_R1_001
        27.7%
        34%
        1.2
        101138LTA_S123_L001_R1_001
        30.5%
        34%
        1.4
        101138LTA_S146_L006_R1_001
        28.1%
        35%
        1.9
        101138LTA_S146_L007_R1_001
        28.1%
        35%
        1.8
        101138NT_S120_L006_R1_001
        41.6%
        38%
        2.2
        101138NT_S120_L007_R1_001
        41.4%
        38%
        2.2
        101138NT_S97_L001_R1_001
        39.5%
        38%
        1.6
        101150LPS_S106_L001_R1_001
        27.7%
        34%
        1.1
        101150LPS_S129_L006_R1_001
        23.6%
        35%
        1.5
        101150LPS_S129_L007_R1_001
        23.8%
        35%
        1.5
        101150LTA_S38_L001_R1_001
        25.0%
        33%
        1.2
        101150LTA_S61_L006_R1_001
        19.9%
        35%
        1.7
        101150LTA_S61_L007_R1_001
        20.0%
        35%
        1.6
        101150NT_S105_L001_R1_001
        31.5%
        37%
        1.2
        101150NT_S128_L006_R1_001
        30.9%
        38%
        1.7
        101150NT_S128_L007_R1_001
        31.0%
        38%
        1.7
        101152LPS_S12_L001_R1_001
        29.8%
        33%
        1.2
        101152LPS_S35_L006_R1_001
        26.6%
        34%
        1.7
        101152LPS_S35_L007_R1_001
        26.9%
        34%
        1.7
        101152LTA_S26_L001_R1_001
        38.2%
        33%
        4.6
        101152LTA_S49_L006_R1_001
        19.1%
        35%
        1.5
        101152LTA_S49_L007_R1_001
        19.2%
        35%
        1.4
        101152NT_S124_L001_R1_001
        33.8%
        36%
        1.3
        101152NT_S147_L006_R1_001
        35.1%
        37%
        1.9
        101152NT_S147_L007_R1_001
        35.0%
        37%
        1.9
        101157LPS_S30_L001_R1_001
        30.0%
        33%
        1.4
        101157LPS_S53_L006_R1_001
        26.9%
        34%
        1.9
        101157LPS_S53_L007_R1_001
        27.0%
        34%
        1.8
        101157LTA_S11_L001_R1_001
        27.5%
        33%
        1.2
        101157LTA_S34_L006_R1_001
        25.7%
        35%
        1.7
        101157LTA_S34_L007_R1_001
        25.9%
        35%
        1.7
        101157NT_S132_L001_R1_001
        30.4%
        35%
        1.3
        101157NT_S155_L006_R1_001
        29.3%
        36%
        1.8
        101157NT_S155_L007_R1_001
        29.5%
        36%
        1.8
        101178LPS_S24_L001_R1_001
        32.0%
        33%
        1.4
        101178LPS_S47_L006_R1_001
        30.4%
        35%
        1.9
        101178LPS_S47_L007_R1_001
        30.4%
        35%
        1.9
        101178LTA_S23_L001_R1_001
        28.1%
        33%
        1.3
        101178LTA_S46_L006_R1_001
        25.4%
        35%
        1.9
        101178LTA_S46_L007_R1_001
        25.5%
        35%
        1.9
        101178NT_S57_L001_R1_001
        31.0%
        37%
        1.2
        101178NT_S80_L006_R1_001
        30.7%
        38%
        1.7
        101178NT_S80_L007_R1_001
        30.6%
        38%
        1.6
        101213LPS_S32_L006_R1_001
        29.6%
        34%
        2.0
        101213LPS_S32_L007_R1_001
        29.6%
        34%
        1.9
        101213LPS_S9_L001_R1_001
        31.7%
        33%
        1.5
        101213LTA_S17_L001_R1_001
        28.4%
        33%
        1.3
        101213LTA_S40_L006_R1_001
        24.2%
        34%
        1.8
        101213LTA_S40_L007_R1_001
        24.1%
        34%
        1.8
        101213NT_S63_L001_R1_001
        33.4%
        35%
        1.2
        101213NT_S86_L006_R1_001
        33.6%
        36%
        1.7
        101213NT_S86_L007_R1_001
        33.6%
        36%
        1.6
        101221LPS_S116_L001_R1_001
        30.3%
        34%
        1.3
        101221LPS_S139_L006_R1_001
        26.6%
        35%
        1.9
        101221LPS_S139_L007_R1_001
        26.8%
        35%
        1.9
        101221LTA_S43_L001_R1_001
        31.0%
        34%
        1.3
        101221LTA_S66_L006_R1_001
        28.3%
        35%
        1.8
        101221LTA_S66_L007_R1_001
        28.3%
        35%
        1.8
        101221NT_S135_L001_R1_001
        35.4%
        36%
        1.2
        101221NT_S158_L006_R1_001
        36.2%
        37%
        1.9
        101221NT_S158_L007_R1_001
        36.2%
        37%
        1.9
        101241LTA_S32_L001_R1_001
        34.7%
        35%
        1.5
        101241LTA_S55_L006_R1_001
        33.9%
        36%
        2.1
        101241LTA_S55_L007_R1_001
        33.8%
        36%
        2.1
        101241NT_S60_L001_R1_001
        36.8%
        36%
        1.3
        101241NT_S83_L006_R1_001
        39.2%
        37%
        2.0
        101241NT_S83_L007_R1_001
        39.2%
        37%
        2.0
        101246LPS_S64_L001_R1_001
        31.5%
        33%
        1.5
        101246LPS_S87_L006_R1_001
        29.3%
        34%
        2.0
        101246LPS_S87_L007_R1_001
        29.3%
        34%
        2.0
        101246LTA_S106_L006_R1_001
        33.2%
        35%
        1.6
        101246LTA_S106_L007_R1_001
        33.1%
        35%
        1.6
        101246LTA_S83_L001_R1_001
        32.1%
        33%
        1.1
        101246NT_S30_L006_R1_001
        29.2%
        37%
        1.6
        101246NT_S30_L007_R1_001
        29.1%
        37%
        1.6
        101246NT_S7_L001_R1_001
        29.9%
        36%
        1.1
        101254LPS_S122_L001_R1_001
        34.4%
        33%
        1.3
        101254LPS_S145_L006_R1_001
        32.7%
        34%
        1.8
        101254LPS_S145_L007_R1_001
        32.8%
        34%
        1.8
        101254LTA_S105_L006_R1_001
        23.2%
        35%
        1.7
        101254LTA_S105_L007_R1_001
        23.3%
        35%
        1.7
        101254LTA_S82_L001_R1_001
        27.5%
        33%
        1.1
        101254NT_S100_L006_R1_001
        30.0%
        37%
        1.3
        101254NT_S100_L007_R1_001
        29.8%
        37%
        1.3
        101254NT_S77_L001_R1_001
        39.9%
        35%
        1.9
        101280LPS_S125_L001_R1_001
        31.2%
        33%
        1.1
        101280LPS_S148_L006_R1_001
        28.2%
        34%
        1.5
        101280LPS_S148_L007_R1_001
        28.2%
        34%
        1.5
        101280LTA_S100_L001_R1_001
        35.2%
        34%
        1.3
        101280LTA_S123_L006_R1_001
        34.3%
        35%
        1.7
        101280LTA_S123_L007_R1_001
        34.2%
        35%
        1.7
        101280NT_S110_L006_R1_001
        30.8%
        38%
        1.5
        101280NT_S110_L007_R1_001
        30.9%
        38%
        1.5
        101280NT_S87_L001_R1_001
        33.2%
        37%
        1.1
        101288LPS_S62_L001_R1_001
        31.9%
        32%
        1.2
        101288LPS_S85_L006_R1_001
        29.3%
        34%
        1.7
        101288LPS_S85_L007_R1_001
        29.5%
        34%
        1.7
        101288LTA_S120_L001_R1_001
        34.6%
        32%
        1.4
        101288LTA_S143_L006_R1_001
        32.7%
        34%
        1.9
        101288LTA_S143_L007_R1_001
        33.2%
        33%
        1.9
        101288NT_S111_L006_R1_001
        23.8%
        38%
        1.6
        101288NT_S111_L007_R1_001
        23.7%
        38%
        1.5
        101288NT_S88_L001_R1_001
        26.6%
        38%
        1.1
        101290LPS_S42_L001_R1_001
        29.9%
        33%
        1.3
        101290LPS_S65_L006_R1_001
        27.7%
        34%
        1.9
        101290LPS_S65_L007_R1_001
        27.6%
        34%
        1.9
        101290LTA_S121_L006_R1_001
        28.9%
        35%
        2.0
        101290LTA_S121_L007_R1_001
        28.9%
        35%
        1.9
        101290LTA_S98_L001_R1_001
        31.0%
        34%
        1.3
        101290NT_S118_L006_R1_001
        29.3%
        37%
        1.6
        101290NT_S118_L007_R1_001
        29.4%
        37%
        1.6
        101290NT_S95_L001_R1_001
        30.8%
        36%
        1.2
        101313LPS_S15_L001_R1_001
        31.1%
        33%
        1.6
        101313LPS_S38_L006_R1_001
        27.3%
        34%
        2.2
        101313LPS_S38_L007_R1_001
        27.4%
        34%
        2.1
        101313LTA_S115_L001_R1_001
        27.7%
        33%
        1.1
        101313LTA_S138_L006_R1_001
        22.7%
        34%
        1.7
        101313LTA_S138_L007_R1_001
        22.8%
        34%
        1.7
        101313NT_S107_L001_R1_001
        32.0%
        35%
        1.4
        101313NT_S130_L006_R1_001
        32.0%
        36%
        1.9
        101313NT_S130_L007_R1_001
        32.1%
        36%
        1.9
        101334LPS_S33_L001_R1_001
        30.5%
        33%
        1.2
        101334LPS_S56_L006_R1_001
        30.2%
        35%
        1.8
        101334LPS_S56_L007_R1_001
        30.6%
        35%
        1.8
        101334LTA_S58_L001_R1_001
        32.5%
        34%
        1.5
        101334LTA_S81_L006_R1_001
        30.6%
        35%
        2.1
        101334LTA_S81_L007_R1_001
        30.5%
        35%
        2.0
        101334NT_S114_L001_R1_001
        38.8%
        37%
        1.4
        101334NT_S137_L006_R1_001
        39.5%
        38%
        1.8
        101334NT_S137_L007_R1_001
        39.5%
        38%
        1.8
        101660LPS_S139_L001_R1_001
        31.8%
        33%
        1.5
        101660LPS_S162_L006_R1_001
        28.8%
        34%
        2.0
        101660LPS_S162_L007_R1_001
        29.0%
        34%
        1.9
        101660NT_S138_L001_R1_001
        30.3%
        35%
        1.2
        101660NT_S161_L006_R1_001
        30.1%
        36%
        1.8
        101660NT_S161_L007_R1_001
        30.1%
        36%
        1.8
        101666LPS_S18_L001_R1_001
        34.1%
        33%
        1.7
        101666LPS_S41_L006_R1_001
        32.8%
        34%
        2.4
        101666LPS_S41_L007_R1_001
        32.9%
        34%
        2.3
        101666NT_S121_L001_R1_001
        35.0%
        35%
        1.3
        101666NT_S144_L006_R1_001
        36.2%
        36%
        1.9
        101666NT_S144_L007_R1_001
        36.5%
        36%
        1.9
        101668LPS_S59_L001_R1_001
        33.4%
        33%
        1.2
        101668LPS_S82_L006_R1_001
        32.8%
        34%
        1.7
        101668LPS_S82_L007_R1_001
        33.1%
        34%
        1.7
        101668LTA_S41_L001_R1_001
        29.9%
        34%
        1.6
        101668LTA_S64_L006_R1_001
        26.5%
        35%
        2.1
        101668LTA_S64_L007_R1_001
        26.6%
        35%
        2.1
        101668NT_S129_L001_R1_001
        30.3%
        35%
        1.3
        101668NT_S152_L006_R1_001
        29.4%
        36%
        1.9
        101668NT_S152_L007_R1_001
        29.6%
        36%
        1.8
        101676LPS_S131_L001_R1_001
        31.9%
        33%
        1.2
        101676LPS_S154_L006_R1_001
        29.7%
        35%
        1.7
        101676LPS_S154_L007_R1_001
        29.9%
        34%
        1.7
        101676LTA_S28_L006_R1_001
        28.4%
        35%
        2.4
        101676LTA_S28_L007_R1_001
        28.3%
        35%
        2.3
        101676LTA_S5_L001_R1_001
        30.7%
        34%
        1.8
        101676NT_S50_L001_R1_001
        37.4%
        36%
        1.3
        101676NT_S73_L006_R1_001
        38.6%
        37%
        1.8
        101676NT_S73_L007_R1_001
        38.6%
        37%
        1.7
        101679LPS_S134_L001_R1_001
        31.3%
        33%
        1.1
        101679LPS_S157_L006_R1_001
        30.6%
        34%
        1.6
        101679LPS_S157_L007_R1_001
        30.7%
        34%
        1.6
        101679LTA_S29_L001_R1_001
        30.0%
        33%
        1.5
        101679LTA_S52_L006_R1_001
        27.6%
        35%
        2.0
        101679LTA_S52_L007_R1_001
        27.6%
        35%
        2.0
        101679NT_S37_L001_R1_001
        34.3%
        36%
        1.0
        101679NT_S60_L006_R1_001
        37.1%
        38%
        1.6
        101679NT_S60_L007_R1_001
        37.0%
        38%
        1.5
        101680LPS_S29_L006_R1_001
        30.4%
        35%
        1.9
        101680LPS_S29_L007_R1_001
        30.5%
        35%
        1.8
        101680LPS_S6_L001_R1_001
        32.4%
        34%
        1.4
        101680LTA_S14_L001_R1_001
        28.8%
        34%
        1.3
        101680LTA_S37_L006_R1_001
        25.5%
        35%
        1.8
        101680LTA_S37_L007_R1_001
        25.4%
        35%
        1.7
        101680NT_S13_L001_R1_001
        49.7%
        37%
        2.5
        101680NT_S36_L006_R1_001
        54.1%
        38%
        3.6
        101680NT_S36_L007_R1_001
        53.9%
        38%
        3.5
        101682LPS_S55_L001_R1_001
        28.2%
        33%
        1.2
        101682LPS_S78_L006_R1_001
        24.5%
        35%
        1.7
        101682LPS_S78_L007_R1_001
        24.7%
        34%
        1.7
        101682LTA_S20_L001_R1_001
        32.5%
        34%
        1.5
        101682LTA_S43_L006_R1_001
        32.0%
        36%
        2.0
        101682LTA_S43_L007_R1_001
        31.8%
        35%
        2.0
        101682NT_S10_L001_R1_001
        39.4%
        36%
        1.4
        101682NT_S33_L006_R1_001
        41.8%
        38%
        2.1
        101682NT_S33_L007_R1_001
        41.9%
        38%
        2.1
        101684LPS_S51_L001_R1_001
        37.1%
        33%
        1.2
        101684LPS_S74_L006_R1_001
        37.2%
        34%
        1.6
        101684LPS_S74_L007_R1_001
        37.2%
        34%
        1.6
        101684NT_S69_L001_R1_001
        45.3%
        37%
        1.3
        101684NT_S92_L006_R1_001
        48.7%
        38%
        1.9
        101684NT_S92_L007_R1_001
        48.8%
        38%
        1.9
        101685LPS_S21_L001_R1_001
        36.7%
        33%
        1.4
        101685LPS_S44_L006_R1_001
        36.3%
        34%
        1.9
        101685LPS_S44_L007_R1_001
        36.4%
        34%
        1.9
        101685NT_S75_L001_R1_001
        43.6%
        36%
        1.7
        101685NT_S98_L006_R1_001
        37.5%
        37%
        1.4
        101685NT_S98_L007_R1_001
        37.6%
        37%
        1.4
        101687LPS_S27_L001_R1_001
        35.0%
        34%
        1.5
        101687LPS_S50_L006_R1_001
        33.6%
        35%
        2.1
        101687LPS_S50_L007_R1_001
        33.6%
        35%
        2.1
        101687LTA_S74_L001_R1_001
        45.8%
        34%
        4.2
        101687LTA_S97_L006_R1_001
        26.1%
        35%
        1.5
        101687LTA_S97_L007_R1_001
        26.0%
        35%
        1.5
        101687NT_S102_L006_R1_001
        32.8%
        38%
        2.0
        101687NT_S102_L007_R1_001
        32.7%
        38%
        2.0
        101687NT_S79_L001_R1_001
        32.1%
        37%
        1.3
        101688LPS_S36_L001_R1_001
        35.0%
        33%
        1.6
        101688LPS_S59_L006_R1_001
        32.6%
        34%
        2.2
        101688LPS_S59_L007_R1_001
        32.6%
        34%
        2.2
        101688LTA_S109_L006_R1_001
        22.0%
        34%
        1.5
        101688LTA_S109_L007_R1_001
        21.7%
        34%
        1.5
        101688LTA_S86_L001_R1_001
        26.8%
        33%
        1.1
        101688NT_S115_L006_R1_001
        40.0%
        38%
        1.8
        101688NT_S115_L007_R1_001
        40.1%
        38%
        1.7
        101688NT_S92_L001_R1_001
        37.7%
        37%
        1.2
        101692LPS_S112_L001_R1_001
        27.1%
        33%
        1.1
        101692LPS_S135_L006_R1_001
        23.5%
        34%
        1.6
        101692LPS_S135_L007_R1_001
        23.4%
        34%
        1.6
        101692NT_S25_L001_R1_001
        35.2%
        37%
        1.5
        101692NT_S48_L006_R1_001
        35.7%
        38%
        2.1
        101692NT_S48_L007_R1_001
        35.5%
        38%
        2.0
        101694LPS_S109_L001_R1_001
        47.6%
        34%
        1.6
        101694LPS_S132_L006_R1_001
        50.8%
        35%
        2.3
        101694LPS_S132_L007_R1_001
        50.9%
        35%
        2.3
        101694LTA_S102_L001_R1_001
        37.5%
        34%
        1.4
        101694LTA_S125_L006_R1_001
        38.6%
        35%
        1.9
        101694LTA_S125_L007_R1_001
        38.8%
        35%
        1.9
        101694NT_S117_L001_R1_001
        38.5%
        36%
        1.2
        101694NT_S140_L006_R1_001
        41.6%
        37%
        1.8
        101694NT_S140_L007_R1_001
        41.9%
        37%
        1.8
        101696LPS_S119_L001_R1_001
        38.9%
        33%
        1.3
        101696LPS_S142_L006_R1_001
        39.9%
        34%
        1.9
        101696LPS_S142_L007_R1_001
        39.8%
        34%
        1.8
        101696NT_S128_L001_R1_001
        28.1%
        33%
        2.6
        101696NT_S151_L006_R1_001
        16.7%
        35%
        1.4
        101696NT_S151_L007_R1_001
        16.9%
        35%
        1.4
        101697LPS_S113_L001_R1_001
        30.0%
        34%
        1.3
        101697LPS_S136_L006_R1_001
        25.7%
        34%
        1.8
        101697LPS_S136_L007_R1_001
        25.6%
        34%
        1.8
        101697LTA_S111_L001_R1_001
        29.4%
        34%
        1.3
        101697LTA_S134_L006_R1_001
        25.8%
        35%
        1.7
        101697LTA_S134_L007_R1_001
        25.8%
        35%
        1.7
        101697NT_S31_L001_R1_001
        28.8%
        36%
        1.3
        101697NT_S54_L006_R1_001
        27.1%
        37%
        1.9
        101697NT_S54_L007_R1_001
        26.9%
        37%
        1.9
        101699LPS_S104_L001_R1_001
        34.7%
        33%
        2.5
        101699LPS_S127_L006_R1_001
        23.4%
        34%
        1.4
        101699LPS_S127_L007_R1_001
        23.4%
        34%
        1.4
        101699NT_S27_L006_R1_001
        39.0%
        37%
        1.9
        101699NT_S27_L007_R1_001
        39.1%
        37%
        1.9
        101699NT_S4_L001_R1_001
        35.8%
        36%
        1.2
        101703LPS_S44_L001_R1_001
        32.5%
        33%
        1.5
        101703LPS_S67_L006_R1_001
        30.6%
        34%
        2.1
        101703LPS_S67_L007_R1_001
        30.4%
        34%
        2.0
        101703LTA_S108_L001_R1_001
        29.5%
        33%
        1.1
        101703LTA_S131_L006_R1_001
        27.5%
        35%
        1.6
        101703LTA_S131_L007_R1_001
        27.5%
        35%
        1.6
        101703NT_S56_L001_R1_001
        31.5%
        36%
        1.2
        101703NT_S79_L006_R1_001
        31.9%
        37%
        1.7
        101703NT_S79_L007_R1_001
        32.1%
        37%
        1.7
        101706LPS_S133_L001_R1_001
        31.7%
        34%
        1.4
        101706LPS_S156_L006_R1_001
        29.4%
        34%
        1.8
        101706LPS_S156_L007_R1_001
        29.5%
        34%
        1.8
        101706LTA_S126_L001_R1_001
        27.5%
        34%
        1.2
        101706LTA_S149_L006_R1_001
        25.2%
        35%
        1.7
        101706LTA_S149_L007_R1_001
        25.0%
        35%
        1.7
        101706NT_S52_L001_R1_001
        49.8%
        35%
        2.8
        101706NT_S75_L006_R1_001
        34.2%
        37%
        1.5
        101706NT_S75_L007_R1_001
        34.3%
        37%
        1.5
        101709LPS_S39_L001_R1_001
        32.1%
        33%
        1.4
        101709LPS_S62_L006_R1_001
        30.6%
        35%
        1.9
        101709LPS_S62_L007_R1_001
        30.7%
        35%
        1.9
        101709LTA_S65_L001_R1_001
        25.6%
        34%
        1.2
        101709LTA_S88_L006_R1_001
        22.3%
        35%
        1.8
        101709LTA_S88_L007_R1_001
        22.2%
        35%
        1.8
        101709NT_S48_L001_R1_001
        32.5%
        35%
        1.5
        101709NT_S71_L006_R1_001
        31.7%
        37%
        2.2
        101709NT_S71_L007_R1_001
        31.8%
        37%
        2.1
        101711LPS_S49_L001_R1_001
        30.6%
        33%
        1.4
        101711LPS_S72_L006_R1_001
        27.6%
        34%
        2.1
        101711LPS_S72_L007_R1_001
        27.7%
        34%
        2.1
        101711LTA_S130_L001_R1_001
        29.5%
        34%
        1.2
        101711LTA_S153_L006_R1_001
        26.7%
        35%
        1.7
        101711LTA_S153_L007_R1_001
        26.8%
        35%
        1.7
        101711NT_S67_L001_R1_001
        31.1%
        36%
        1.2
        101711NT_S90_L006_R1_001
        31.3%
        37%
        1.7
        101711NT_S90_L007_R1_001
        31.2%
        37%
        1.7
        101712LPS_S46_L001_R1_001
        29.8%
        33%
        1.4
        101712LPS_S69_L006_R1_001
        26.4%
        34%
        1.8
        101712LPS_S69_L007_R1_001
        26.6%
        34%
        1.8
        101712LTA_S61_L001_R1_001
        28.4%
        34%
        1.3
        101712LTA_S84_L006_R1_001
        26.3%
        35%
        1.8
        101712LTA_S84_L007_R1_001
        26.1%
        35%
        1.8
        101712NT_S71_L001_R1_001
        40.1%
        36%
        1.5
        101712NT_S94_L006_R1_001
        42.0%
        37%
        2.2
        101712NT_S94_L007_R1_001
        42.1%
        37%
        2.1
        101713LPS_S113_L006_R1_001
        29.5%
        36%
        1.3
        101713LPS_S113_L007_R1_001
        29.7%
        35%
        1.3
        101713LPS_S90_L001_R1_001
        39.5%
        34%
        1.9
        101713LTA_S47_L001_R1_001
        30.2%
        34%
        1.5
        101713LTA_S70_L006_R1_001
        28.2%
        35%
        2.1
        101713LTA_S70_L007_R1_001
        28.1%
        35%
        2.1
        101713NT_S104_L006_R1_001
        31.1%
        38%
        1.9
        101713NT_S104_L007_R1_001
        31.1%
        38%
        1.9
        101713NT_S81_L001_R1_001
        31.3%
        37%
        1.3
        101716LPS_S103_L006_R1_001
        29.5%
        35%
        1.9
        101716LPS_S103_L007_R1_001
        29.7%
        35%
        1.8
        101716LPS_S80_L001_R1_001
        31.2%
        34%
        1.3
        101716NT_S108_L006_R1_001
        33.0%
        38%
        2.1
        101716NT_S108_L007_R1_001
        32.9%
        38%
        2.1
        101716NT_S85_L001_R1_001
        33.5%
        37%
        1.5
        101717LPS_S72_L001_R1_001
        30.4%
        34%
        1.3
        101717LPS_S95_L006_R1_001
        25.9%
        35%
        1.3
        101717LPS_S95_L007_R1_001
        25.8%
        35%
        1.3
        101717NT_S103_L001_R1_001
        34.9%
        36%
        1.4
        101717NT_S126_L006_R1_001
        34.6%
        37%
        1.9
        101717NT_S126_L007_R1_001
        34.4%
        36%
        1.8
        101724LPS_S70_L001_R1_001
        37.4%
        34%
        1.9
        101724LPS_S93_L006_R1_001
        37.6%
        35%
        2.7
        101724LPS_S93_L007_R1_001
        37.7%
        35%
        2.6
        101724NT_S110_L001_R1_001
        36.1%
        35%
        1.0
        101724NT_S133_L006_R1_001
        41.5%
        37%
        1.7
        101724NT_S133_L007_R1_001
        41.4%
        36%
        1.6
        101725LPS_S68_L001_R1_001
        37.3%
        34%
        1.4
        101725LPS_S91_L006_R1_001
        37.9%
        35%
        1.9
        101725LPS_S91_L007_R1_001
        38.1%
        35%
        1.9
        101725LTA_S54_L001_R1_001
        39.9%
        33%
        1.3
        101725LTA_S77_L006_R1_001
        42.4%
        35%
        2.0
        101725LTA_S77_L007_R1_001
        42.9%
        35%
        2.0
        101725NT_S40_L001_R1_001
        33.9%
        35%
        1.4
        101725NT_S63_L006_R1_001
        34.1%
        36%
        2.0
        101725NT_S63_L007_R1_001
        34.3%
        36%
        2.0
        101728LPS_S119_L006_R1_001
        27.6%
        35%
        1.7
        101728LPS_S119_L007_R1_001
        27.6%
        35%
        1.7
        101728LPS_S96_L001_R1_001
        30.6%
        34%
        1.2
        101728LTA_S53_L001_R1_001
        31.6%
        34%
        1.2
        101728LTA_S76_L006_R1_001
        29.8%
        35%
        1.7
        101728LTA_S76_L007_R1_001
        29.9%
        35%
        1.6
        101728NT_S28_L001_R1_001
        32.3%
        36%
        1.4
        101728NT_S51_L006_R1_001
        33.5%
        37%
        2.0
        101728NT_S51_L007_R1_001
        33.3%
        37%
        2.0
        101730LPS_S107_L006_R1_001
        38.8%
        36%
        1.5
        101730LPS_S107_L007_R1_001
        39.1%
        36%
        1.5
        101730LPS_S84_L001_R1_001
        44.8%
        34%
        1.7
        101730LTA_S31_L006_R1_001
        32.4%
        36%
        1.8
        101730LTA_S31_L007_R1_001
        32.5%
        36%
        1.8
        101730LTA_S8_L001_R1_001
        32.6%
        35%
        1.3
        101730NT_S34_L001_R1_001
        33.1%
        36%
        1.4
        101730NT_S57_L006_R1_001
        33.2%
        37%
        2.1
        101730NT_S57_L007_R1_001
        33.1%
        37%
        2.0
        101734LPS_S141_L001_R1_001
        51.0%
        32%
        1.2
        101734LPS_S164_L006_R1_001
        53.9%
        32%
        1.6
        101734LPS_S164_L007_R1_001
        54.0%
        32%
        1.5
        101734NT_S140_L001_R1_001
        57.2%
        35%
        1.5
        101734NT_S163_L006_R1_001
        62.2%
        36%
        2.1
        101734NT_S163_L007_R1_001
        61.9%
        35%
        2.1
        101736LPS_S66_L001_R1_001
        30.4%
        34%
        1.2
        101736LPS_S89_L006_R1_001
        29.3%
        35%
        1.8
        101736LPS_S89_L007_R1_001
        29.6%
        35%
        1.7
        101736NT_S22_L001_R1_001
        37.6%
        37%
        1.4
        101736NT_S45_L006_R1_001
        40.0%
        38%
        2.1
        101736NT_S45_L007_R1_001
        39.8%
        38%
        2.0
        101738LPS_S76_L001_R1_001
        47.4%
        35%
        1.4
        101738LPS_S99_L006_R1_001
        52.0%
        37%
        2.0
        101738LPS_S99_L007_R1_001
        51.8%
        37%
        2.0
        101738NT_S19_L001_R1_001
        45.6%
        36%
        1.4
        101738NT_S42_L006_R1_001
        49.4%
        38%
        2.0
        101738NT_S42_L007_R1_001
        49.2%
        38%
        2.0
        101739LPS_S101_L006_R1_001
        29.6%
        35%
        1.7
        101739LPS_S101_L007_R1_001
        29.8%
        35%
        1.7
        101739LPS_S78_L001_R1_001
        31.7%
        34%
        1.2
        101739NT_S16_L001_R1_001
        25.8%
        36%
        1.0
        101739NT_S39_L006_R1_001
        24.5%
        38%
        1.6
        101739NT_S39_L007_R1_001
        24.7%
        38%
        1.6
        101746LPS_S116_L006_R1_001
        42.8%
        36%
        1.8
        101746LPS_S116_L007_R1_001
        42.8%
        36%
        1.8
        101746LPS_S93_L001_R1_001
        39.9%
        34%
        1.3
        101746LTA_S35_L001_R1_001
        39.3%
        34%
        1.5
        101746LTA_S58_L006_R1_001
        40.5%
        35%
        2.1
        101746LTA_S58_L007_R1_001
        40.6%
        35%
        2.0
        101746NT_S45_L001_R1_001
        37.0%
        36%
        1.1
        101746NT_S68_L006_R1_001
        38.5%
        37%
        1.5
        101746NT_S68_L007_R1_001
        38.6%
        37%
        1.5

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        loading..

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        loading..

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        loading..

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
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        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

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        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

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        Sequence Length Distribution

        All samples have sequences of a single length (101bp).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

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        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        423 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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